2F3K | pdb_00002f3k

Substrate envelope and drug resistance: crystal structure of r01 in complex with wild-type hiv-1 protease

• PDB DOI: https://doi.org/10.2210/pdb2F3K/pdb

• Classification: HYDROLASE
• Organism(s): Human immunodeficiency virus 1
• Mutation(s): Yes 


• Deposited: 2005-11-21 Released: 2006-11-21 
• Deposition Author(s): Prabu-Jeyabalan, M., King, N.M., Nalivaika, E.A., Heilek-Snyder, G., Cammack, N., Schiffer, C.A.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.60 Å
• R-Value Free: 
  0.197 (Depositor), 0.206 (DCC) 
• R-Value Work: 
  0.163 (Depositor), 0.175 (DCC) 
• R-Value Observed: 
  0.165 (Depositor) 

Starting Model: experimental

Literature

Substrate envelope and drug resistance: crystal structure of RO1 in complex with wild-type human immunodeficiency virus type 1 protease.

Prabu-Jeyabalan, M., King, N.M., Nalivaika, E.A., Heilek-Snyder, G., Cammack, N., Schiffer, C.A.

(2006) Antimicrob Agents Chemother 50: 1518-1521

• PubMed: 16569872 
• DOI: https://doi.org/10.1128/AAC.50.4.1518-1521.2006
• Primary Citation Related Structures: 
  2F3K


• PubMed Abstract: 
  

  In our previous crystallographic studies of human immunodeficiency virus type 1 (HIV-1) protease-substrate complexes, we described a conserved "envelope" that appears to be important for substrate recognition and the selection of drug-resistant mutations. In this study, the complex of HIV-1 protease with the inhibitor RO1 was determined and comparison with the substrate envelope provides a rationale for mutational patterns.

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Organizational Affiliation: 
• Department of Biochemistry & Molecular Pharmacology, University of Massachusetts Medical School, 364 Plantation St., Worcester, MA 01605, USA.

Biological Assembly 1  

Global Symmetry: Cyclic - C2  (Explore in 3D)
Global Stoichiometry: Homo 2-mer - A2 

Biological assembly 1 assigned by authors and generated by PISA (software)

Macromolecule Content 

• Total Structure Weight: 22.82 kDa 
• Atom Count: 2,168 
• Modeled Residue Count: 198 
• Deposited Residue Count: 198 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Protease	A, B	99	Human immunodeficiency virus 1	Mutation(s): 1  EC: 3.4.23.16
UniProt
Find proteins for P03369 (Human immunodeficiency virus type 1 group M subtype B (isolate ARV2/SF2)) Explore P03369  Go to UniProtKB:  P03369

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
RO1	F [auth A]	(3S,4AS,8AS)-N-(TERT-BUTYL)-2-[(3S)-3-({3-(METHYLSULFONYL)-N-[(PYRIDIN-3-YLOXY)ACETYL]-L-VALYL}AMINO)-2-OXO-4-PHENYLBUTYL]DECAHYDROISOQUINOLINE-3-CARBOXAMIDE C37 H53 N5 O7 S NHCWVIKQVTUOGE-HAMVXVSQSA-N
PO4	C [auth A], D [auth A], E [auth A], G [auth B], H [auth B]	PHOSPHATE ION O4 P NBIIXXVUZAFLBC-UHFFFAOYSA-K

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.60 Å
• R-Value Free:  0.197 (Depositor), 0.206 (DCC) 
• R-Value Work:  0.163 (Depositor), 0.175 (DCC) 
• R-Value Observed: 0.165 (Depositor) 

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 50.873	α = 90
b = 58.167	β = 90
c = 61.653	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
SCALEPACK	data scaling
AMoRE	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2006-11-21 
Deposition Author(s): Prabu-Jeyabalan, M., King, N.M., Nalivaika, E.A., Heilek-Snyder, G., Cammack, N., Schiffer, C.A.

Revision History  

• Version 1.0: 2006-11-21
  Type: Initial release
  
• Version 1.1: 2008-05-01
  Changes: Version format compliance
• Version 1.2: 2011-07-13
  Changes: Version format compliance
• Version 1.3: 2017-10-18
  Changes: Refinement description
• Version 1.4: 2021-10-20
  Changes: Database references, Derived calculations
• Version 1.5: 2023-08-23
  Changes: Data collection, Refinement description